Kirchdoerfer Lab
Home of the Robert Kirchdoerfer lab

Publications

  1. Anderson TK, Hoferle PJ, Chojnacki KJ, Lee KW, Coon JJ, Kirchdoerfer RN. An alphacoronavirus polymerase structure reveals conserved replication factor functions. Nucleic Acids Res 2024 Mar 5:gkae153. doi: 10.1093/nar/gkae153. PMID: 38442273
  2. Chen DY, Kenney D, Chin CV, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O’Connell AK, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation.Nature 2023 Mar;615(7950):143-150. doi: 10.1038/s41586-023-05697-2. PMID: 36630998.
  3. Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa IM, Passow KT, Kennelly SA, Moorthy R, Dulin D, Feng JY, Harki DA, Kirchdoerfer RN, Cameron CE, Arnold JJ. Interfering with nucleotide excision by the coronavirus 3′-to-5′ exoribonuclease. Nucleic Acids Res
    . 2023 Jan 11;51(1):315-336. doi: 10.1093/nar/gkac1177. PMID: 36546762 PMCID: PMC9841423
  4. Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB. From structure to sequence: Antibody discovery using cryoEM. Sci Adv. 2022 Jan 21;8(3):eabk2039. doi: 10.1126/sciadv.abk2039. Epub 2022 Jan 19. PMID: 35044813; PMCID: PMC8769551.
  5. Seifert M, Bera SC, van Nies P, Kirchdoerfer RN, Shannon A, Le TT, Meng X, Xia H, Wood JM, Harris LD, Papini FS, Arnold JJ, Almo S, Grove TL, Shi PY, Xiang Y, Canard B, Depken M, Cameron CE, Dulin D. Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective. Elife. 2021 Oct 7;10:e70968. doi: 10.7554/eLife.70968. PMID: 34617885; PMCID: PMC8497053.
  6. Bera SC, Seifert M, Kirchdoerfer RN, van Nies P, Wubulikasimu Y, Quack S, Papini FS, Arnold JJ, Canard B, Cameron CE, Depken M, Dulin D. The nucleotide addition cycle of the SARS-CoV-2 polymerase. Cell Rep. 2021 Aug 31;36(9):109650. doi: 10.1016/j.celrep.2021.109650. Epub 2021 Aug 17. PMID: 34433083; PMCID: PMC8367775.
  7. Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, et al. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci. 2021 May 10;8:653148. doi: 10.3389/fmolb.2021.653148. eCollection 2021. PMID: 34041264; PMCID: PMC8141814.
  8. Seifert M, Bera SC, van Nies P, Kirchdoerfer RN, Shannon A, Le TT, Meng X, Xia H, Wood JM, Harris LD, Papini FS, Arnold JJ, Almo SC, Grove TL, Shi PY, Xiang Y, Canard B, Depken M, Cameron CE, Dulin D. Inhibition of SARS-CoV-2 polymerase by nucleotide analogs: a single molecule perspective. bioRxiv. 2021 Apr 8:2020.08.06.240325. doi: 10.1101/2020.08.06.240325. Preprint. PMID: 33851161; PMCID: PMC8043451.
  9. Tonelli M, Rienstra C, Anderson TK, Kirchdoerfer R, Henzler-Wildman K. 1H, 13C, and 15N backbone and side chain chemical shift assignments of the SARS-CoV-2 non-structural protein 7. Biomol NMR Assign. 2021 Apr;15(1):73-77. doi: 10.1007/s12104-020-09985-0. Epub 2020 Nov 20. PMID: 33219414; PMCID: PMC7678775.
  10. Bera SC, Seifert M, Kirchdoerfer RN, van Nies P, Wubulikasimu Y, Quack S, Papini FS, Arnold JJ, Canard B, Cameron CE, Depken M, Dulin D. The nucleotide addition cycle of the SARS-CoV-2 polymerase. bioRxiv. 2021 Mar 27:2021.03.27.437309. doi: 10.1101/2021.03.27.437309. Preprint. PMID: 33791706; PMCID: PMC8010733.
  11. Conti BJ, Leicht AS, Kirchdoerfer RN, Sussman MR. Mass spectrometric based detection of protein nucleotidylation in the RNA polymerase of SARS-CoV-2. Commun Chem. 2021;4:41. doi: 10.1038/s42004-021-00476-4. Epub 2021 Mar 19. PMID: 34189273; PMCID: PMC8238455.
  12. Kirchdoerfer RN, Bhandari M, Martini O, Sewall LM, Bangaru S, Yoon KJ, Ward AB. Structure and immune recognition of the porcine epidemic diarrhea virus spike protein. Structure. 2021 Apr 1;29(4):385-392.e5. doi: 10.1016/j.str.2020.12.003. Epub 2020 Dec 29. PMID: 33378641; PMCID: PMC7962898.
  13. Ju J, Li X, Kumar S, Jockusch S, Chien M, Tao C, Morozova I, Kalachikov S, Kirchdoerfer RN, Russo JJ. Nucleotide analogues as inhibitors of SARS-CoV Polymerase. Pharmacol Res Perspect. 2020 Dec;8(6):e00674. doi: 10.1002/prp2.674. PMID: 33124786; PMCID: PMC7596664.
  14. Chien M, Anderson TK, Jockusch S, Tao C, Li X, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J. Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19. J Proteome Res. 2020 Nov 6;19(11):4690-4697. doi: 10.1021/acs.jproteome.0c00392. Epub 2020 Aug 5. PMID: 32692185; PMCID: PMC7640960.
  15. Jockusch S, Tao C, Li X, Anderson TK, Chien M, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J. A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19. Antiviral Res. 2020 Aug;180:104857. doi: 10.1016/j.antiviral.2020.104857. Epub 2020 Jun 18. PMID: 32562705; PMCID: PMC7299870.
  16. Kirchdoerfer RN. Halting coronavirus polymerase. J Biol Chem. 2020 Apr 10;295(15):4780-4781. doi: 10.1074/jbc.H120.013397. PMID: 32277065; PMCID: PMC7152748.
  17. Nogal B, Bianchi M, Cottrell CA, Kirchdoerfer RN, Sewall LM, Turner HL, Zhao F, Sok D, Burton DR, Hangartner L, Ward AB. Mapping Polyclonal Antibody Responses in Non-human Primates Vaccinated with HIV Env Trimer Subunit Vaccines. Cell Rep. 2020 Mar 17;30(11):3755-3765.e7. doi: 10.1016/j.celrep.2020.02.061. PMID: 32187547; PMCID: PMC7153566.
  18. Lin AE, Diehl WE, Cai Y, Finch CL, Akusobi C, Kirchdoerfer RN, Bollinger L, Schaffner SF, Brown EA, Saphire EO, Andersen KG, Kuhn JH, Luban J, Sabeti PC. Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111. Viruses. 2020 Jan 15;12(1).doi: 10.3390/v12010105. PMID: 31952352; PMCID: PMC7019320.
  19. Wang N, Rosen O, Wang L, Turner HL, Stevens LJ, Corbett KS, Bowman CA, Pallesen J, Shi W, Zhang Y, Leung K, Kirchdoerfer RN, Becker MM, Denison MR, Chappell JD, Ward AB, Graham BS, McLellan JS. Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD. Cell Rep. 2019 Sep 24;28(13):3395-3405.e6. doi: 10.1016/j.celrep.2019.08.052. PMID: 31553909.
  20. Kirchdoerfer RN, Ward AB. Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nat Commun. 2019 May 28;10(1):2342. doi: 10.1038/s41467-019-10280-3. PMID: 31138817; PMCID: PMC6538669.
  21. Kirchdoerfer RN, Saphire EO, Ward AB. Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex. Acta Crystallogr F Struct Biol Commun. 2019 May 1;75(Pt 5):340-347. doi: 10.1107/S2053230X19004424. Epub 2019 Apr 24. PMID: 31045563;  PMCID: PMC6497097.
  22. Kirchdoerfer RN, Wang N, Pallesen J, Wrapp D, Turner HL, Cottrell CA, Corbett KS, Graham BS, McLellan JS, Ward AB. Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis. Sci Rep. 2018 Oct 24;8(1):15701. doi: 10.1038/s41598-018-34171-7. PMID: 30356097; PMCID: PMC6200764.
  23. King LB, Fusco ML, Flyak AI, Ilinykh PA, Huang K, Gunn B, Kirchdoerfer RN, Hastie KM, Sangha AK, Meiler J, Alter G, Bukreyev A, Crowe JE Jr, Saphire EO. The Marburgvirus-Neutralizing Human Monoclonal Antibody MR191 Targets a Conserved Site to Block Virus Receptor Binding. Cell Host Microbe. 2018 Jan 10;23(1):101-109.e4. doi: 10.1016/j.chom.2017.12.003. PMID: 29324225; PMCID: PMC5772738.
  24. Pallesen J, Wang N, Corbett KS, Wrapp D, Kirchdoerfer RN, Turner HL, Cottrell CA, Becker MM, Wang L, Shi W, Kong WP, Andres EL, Kettenbach AN, Denison MR, Chappell JD, Graham BS, Ward AB, McLellan JS. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7348-E7357. doi: 10.1073/pnas.1707304114. Epub 2017 Aug 14. PMID: 28807998; PMCID: PMC5584442.
  25. Kirchdoerfer RN, Wang N, Pallesen J, Wrapp D, Turner HL, Cottrell CA, Corbett KS, Graham BS, McLellan JS, Ward AB. Structural insights into the SARS Spike-ACE2 receptor complex. American Society for Virology Annual Meeting; 2017 June 24; Madison, WI, United States.
  26. Kirchdoerfer RN, Wang N, Pallesen J, Wrapp D, Turner HL, Cottrell CA, Corbett KS, Graham BS, McLellan JS, Ward AB. The SARS Spike-ACE2 Receptor Complex. In: Kirchdoerfer, editor. Nidovirus2017; 2017 June 3; Kansas City, MO, United States.
  27. Bruhn JF, Kirchdoerfer RN, Urata SM, Li S, Tickle IJ, Bricogne G, Saphire EO. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain. J Virol. 2017 Jan 15;91(2). doi: 10.1128/JVI.01085-16. Print 2017 Jan 15. PMID: 27847355; PMCID: PMC5215338.
  28. Kirchdoerfer RN, Wasserman H, Amarasinghe GK, Saphire EO. Filovirus Structural Biology: The Molecules in the Machine. Curr Top Microbiol Immunol. 2017;411:381-417. doi: 10.1007/82_2017_16. Review. PMID: 28795188.
  29. Kirchdoerfer RN, Moyer CL, Abelson DM, Saphire EO. The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis. PLoS Pathog. 2016 Oct;12(10):e1005937. doi: 10.1371/journal.ppat.1005937. eCollection 2016 Oct. PMID: 27755595; PMCID: PMC5068707.
  30. Kirchdoerfer RN, Moyer CL, Abelson DM, Saphire EO. The Ebola virus VP30-NP interaction is a regulator of viral RNA synthesis. American Society for Virology Annual Meeting; 2016 June 19; Blacksburg, VA, United States. c2016.
  31. Kirchdoerfer RN, Cottrell CA, Wang N, Pallesen J, Yassine HM, Turner HL, Corbett KS, Graham BS, McLellan JS, Ward AB. Pre-fusion structure of a human coronavirus spike protein. Keystone Positive Sense RNA Viruses Meeting; 2016 May 1; Austin, TX, United States. c2016.
  32. Kirchdoerfer RN, Cottrell CA, Wang N, Pallesen J, Yassine HM, Turner HL, Corbett KS, Graham BS, McLellan JS, Ward AB. Pre-fusion structure of a human coronavirus spike protein. Nature. 2016 Mar 3;531(7592):118-21. doi: 10.1038/nature17200. PubMed PMID: 26935699; PubMed Central PMCID: PMC4860016.
  33. Kirchdoerfer RN, Abelson DM, Li S, Wood MR, Saphire EO. Ebola virus Nucleoprotein Assembly. American Society for Virology 34th Annual Meeting; 2015 July 11; London, ON, Canada. c2015.
  34. Kirchdoerfer RN, Abelson DM, Li S, Wood MR, Saphire EO. Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex. Cell Rep. 2015 Jul 7;12(1):140-149. doi: 10.1016/j.celrep.2015.06.003. Epub 2015 Jun 25. PMID: 26119732; PMCID: PMC4500542.
  35. Clifton MC, Kirchdoerfer RN, Atkins K, Abendroth J, Raymond A, Grice R, Barnes S, Moen S, Lorimer D, Edwards TE, Myler PJ, Saphire EO. Structure of the Reston ebolavirus VP30 C-terminal domain. Acta Crystallogr F Struct Biol Commun. 2014 Apr;70(Pt 4):457-60. doi: 10.1107/S2053230X14003811. Epub 2014 Mar 25. PMID: 24699737; PMCID: PMC3976061.
  36. Kirchdoerfer RN, Wilson IA. Crystallization of an Influenza Nucleoprotein-RNA Complex. American Crystallographic Association; 2013 July 20; Honolulu, HI, United States. c2013.
  37. Lee JY, Kim HS, Baek IW, Back JM, Han MR, Kong SY, Kim JH, Kirchdoerfer RN, Kim JO, Cooper MD, Wilson IA, Kim HJ, Han BW. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the variable lymphocyte receptor 2913 ectodomain fused with internalin B. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jan 1;69(Pt 1):39-41. doi: 10.1107/S1744309112045484. Epub 2012 Dec 20. PMID: 23295483; PMCID: PMC3539700.
  38. Moeller A, Kirchdoerfer RN, Potter CS, Carragher B, Wilson IA. Organization of the influenza virus replication machinery. Science. 2012 Dec 21;338(6114):1631-4. doi: 10.1126/science.1227270. Epub 2012 Nov 22. PMID: 23180774; PMCID: PMC3578580.
  39. Kirchdoerfer RN, Moeller A, Brock A, Potter CS, Carragher B, Wilson IA. Organization of the Influenza Replication Machinery. American Society for Virology 31st Annual Meeting; 2012 July 21; Madison, WI, United States. c2012.
  40. Kirchdoerfer RN, Herrin BR, Han BW, Turnbough CL Jr, Cooper MD, Wilson IA. Variable lymphocyte receptor recognition of the immunodominant glycoprotein of Bacillus anthracis spores. Structure. 2012 Mar 7;20(3):479-86. doi: 10.1016/j.str.2012.01.009. PMID: 22405006; PMCID: PMC3337218.
  41. Kirchdoerfer RN, Garner AL, Flack CE, Mee JM, Horswill AR, Janda KD, Kaufmann GF, Wilson IA. Structural basis for ligand recognition and discrimination of a quorum-quenching antibody. J Biol Chem. 2011 May 13;286(19):17351-8. doi: 10.1074/jbc.M111.231258. Epub 2011 Mar 23. PMID: 21454495; PMCID: PMC3089576.
  42. Ellis JP, Bakke CK, Kirchdoerfer RN, Jungbauer LM, Cavagnero S. Chain dynamics of nascent polypeptides emerging from the ribosome. ACS Chem Biol. 2008 Sep 19;3(9):555-66. doi: 10.1021/cb800059u. Epub 2008 Aug 22. PMID: 18717565; PMCID: PMC2572860.
  43. Debler EW, Kaufmann GF, Kirchdoerfer RN, Mee JM, Janda KD, Wilson IA. Crystal structures of a quorum-quenching antibody. J Mol Biol. 2007 May 18;368(5):1392-402. doi: 10.1016/j.jmb.2007.02.081. Epub 2007 Mar 6. PMID: 17400249; PMCID: PMC1994716.
  44. Kirchdoerfer RN, Huang JJ, Isola MK, Cavagnero S. Fluorescence-based analysis of aminoacyl- and peptidyl-tRNA by low-pH sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Anal Biochem. 2007 May 1;364(1):92-4. doi: 10.1016/j.ab.2007.01.019. Epub 2007 Jan 19. PMID: 17368419; PMCID: PMC2693959.

External Publication Links